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Demographic inference from whole genomes
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comparing scrm and smcsmcSCRM, recombination process diff, do not produce the same tree #31

Closed shajoezhu closed 8 years ago

shajoezhu commented 9 years ago

compare 

./smcsmcSCRM_dbg -nsam 2 -Np 1 -r 30 130000 -seed 1 -T | less

and 

./scrm_dbg 2 1 -r 30 130000 -seed 1 -T -l 0 | less
shajoezhu commented 9 years ago

compare 

./smcsmcSCRM_dbg -nsam 2 -Np 1 -r 30 130000 -seed 1 -T | less

and 

./scrm_dbg 2 1 -r 30 130000 -seed 1 -T -l 0 | less

at the tenth recombination, the recombination points start to differ

./smcsmcSCRM_dbg -nsam 2 -Np 1 -r 30 130000 -seed 1 -T | less
===== BUILDING NEXT GENEALOGY =====
        scrm Segment Nr: 10 | Sequence position: 20685.66
╦   ╦ -       0 - 2:0x7f2c1e3e6080(0) 1:0x7f2c1e3e6010(0) 
║ ┬ ║ - 33944.1 - 0x7f2c1e3e60f0(0) old 
╚╦┘ ║ - 35127.21 - 0x7f2c1e3e6240(0) 
 ╚═╦╝ - 45795.47 - 0x7f2c1e3e62b0(0) 
        scrm * Recombination at height 1876.245 (above 0x7f2c1e3e6010)
        scrm * Cutting subtree below recombination 
        scrm * * New leaf of local tree: 0x7f2c1e3e61d0
        scrm * * New root of subtree: 0x7f2c1e3e6160
        scrm * * Done
╦    ╦  -       0 - 2:0x7f2c1e3e6080(0) 1:0x7f2c1e3e6010(0) 
║   ┬╚╦ - 1876.245 - 0x7f2c1e3e61d0(0) 0x7f2c1e3e6160(0) 
║ ┬ │   - 33944.1 - 0x7f2c1e3e60f0(0) old 
╚╦┘ │   - 35127.21 - 0x7f2c1e3e6240(0) 
 ╚═╦┘   - 45795.47 - 0x7f2c1e3e62b0(0) 
        scrm * Starting coalescence
        scrm * * * PRUNING: Removing branch above 0x7f2c1e3e60f0 from tree (old)
        scrm * * * PRUNING: Removing node 0x7f2c1e3e6240 from tree (unneeded)
        scrm * * Time interval: 1876.245 - 45795.47 (Last event at 1876.245)
        scrm * * * Active Nodes: a0:0x7f2c1e3e6160:s1(p0) a1:0x7f2c1e3e62b0:s0(p0)
        scrm * * * Total Rates: 0.0001 0 0
        scrm * * * Event at time 15278.95: Coalesence of a0
    ForestState Start Recording 
    ForestState     EventRecorder Event CoalMigr w=2 [20685.66] pop=0 t=1876.245-15278.95 (**COAL**) 
    ForestState Finish recording of event.

./scrm_dbg 2 1 -r 30 130000 -seed 1 -T -l 0 | less
===== BUILDING NEXT GENEALOGY =====
        scrm Segment Nr: 10 | Sequence position: 20685.66
╦   ╦   -       0 - 2:0x7fd34c694080(0) 1:0x7fd34c694010(0) 
║   ║ ┬ - 2741.986 - 0x7fd34c6941d0(0) old 
║   ╚╦┘ - 12093.56 - 0x7fd34c694160(0) 
║ ┬  ║  - 33944.1 - 0x7fd34c694400(0) old 
╚╦┘  ║  - 35127.21 - 0x7fd34c694390(0) 
 ╚═╦═╝  - 45795.47 - 0x7fd34c694320(0) 
        scrm * Recombination at height 13969.81 (above 0x7fd34c694160)
        scrm * Cutting subtree below recombination 
        scrm * * New leaf of local tree: 0x7fd34c6940f0
        scrm * * New root of subtree: 0x7fd34c6942b0
        scrm * * Done
╦    ╦    -       0 - 2:0x7fd34c694080(0) 1:0x7fd34c694010(0) 
║    ║ ┬  - 2741.986 - 0x7fd34c6941d0(0) old 
║    ╚╦┘  - 12093.56 - 0x7fd34c694160(0) 
║   ┬ ╚═╦ - 13969.81 - 0x7fd34c6940f0(0) 0x7fd34c6942b0(0) 
║ ┬ │     - 33944.1 - 0x7fd34c694400(0) old 
╚╦┘ │     - 35127.21 - 0x7fd34c694390(0) 
 ╚═╦┘     - 45795.47 - 0x7fd34c694320(0) 
        scrm * Starting coalescence
        scrm * * * PRUNING: Removing branch above 0x7fd34c694400 from tree (old)
        scrm * * * PRUNING: Removing node 0x7fd34c694390 from tree (unneeded)
        scrm * * Time interval: 13969.81 - 45795.47 (Last event at 13969.81)
        scrm * * * Active Nodes: a0:0x7fd34c6942b0:s1(p0) a1:0x7fd34c694320:s0(p0)
        scrm * * * Total Rates: 0.0001 0 0
        scrm * * * Event at time 27372.52: Coalesence of a0
        scrm * * * Above node 0x7fd34c6940f0
shajoezhu commented 9 years ago

smcsmc is pruning to often, when record_Recombevent_b4_extension, it requires to loop through TimeIntervalIterator, of which scrm originally uses it when sampling coalescent, prune off old branches when as it proceed, here we just looping through the time intervals, should not prune.

gerton commented 9 years ago

Good find. We used to have this bug, and fixed it by setting a do_not_prune flag when iterating from scrm. Apparently this is no longer there, or we are now using the iterator in a different place and forgot to set this flag.

BW Gerton

On 20 Oct 2015, at 16:14, Joe Zhu notifications@github.com wrote:

smcsmc is pruning to often, when record_Recombevent_b4_extension, it requires to loop through TimeIntervalIterator, of which scrm originally uses it when sampling coalescent, prune off old branches when as it proceed, here we just looping through the time intervals, should not prune.

— Reply to this email directly or view it on GitHub https://github.com/luntergroup/smcsmc/issues/31#issuecomment-149597429.

shajoezhu commented 9 years ago

Hi Gerton

Thanks! Yes, that was what I figured. fixed partially, works for two samples, but stuck at three samples atm.

shajoezhu commented 9 years ago

C.I. reports:

$ ./check_smcsmcSCRM_vs_scrm.sh
Testing smcsmcSCRM 
 smcsmcSCRM -nsam 2 -Np 1 -r 130 1000000 ..........
 smcsmcSCRM -nsam 3 -Np 1 -r 130 1000000 ..........
 smcsmcSCRM -nsam 4 -Np 1 -r 130 1000000 ..........
 smcsmcSCRM -nsam 5 -Np 1 -r 130 1000000 ..........
 smcsmcSCRM -nsam 6 -Np 1 -r 130 1000000 ....1c1
< (((1:0.19922,5:0.19922):0.390519,(2:0.089042,(3:0.00674687,6:0.00674687):0.0822952):0.500697):0.0544305,4:0.644169);
---
> (((1:0.19922,5:0.19922):0.390519,(2:0.089042,(3:0.00674687,6:0.00674687):0.0822952):0.500697):0.266101,4:0.85584);
Failed at random seed:  4
Testing for Last tree in scrm and smcsmc.
../scrm  6 1 -r 130 1000000 -T -l 0 -seed 4
../smcsmcSCRM  -nsam 6 -Np 1 -r 130 1000000 -seed 4
shajoezhu commented 9 years ago

The previous test failed at the last position when printing out the newick format tree, as the last recombination happens at position 

===== BUILDING NEXT GENEALOGY =====
        scrm Segment Nr: 305 | Sequence position: 999999.1
   ╦   ╦ ╦ ╦ ╦ ╦   -       0 - 1:0x7f73ff459010(0) 5:0x7f73ff459320(0) 2:0x7f73ff459080(0) 3:0x7f73ff459160(0) 6:0x7f73ff459400(0) 4:0x7f73ff459240(0) 
   ║   ║ ║ ╚╦╝ ║   - 269.8746 - 0x7f73ff459860(0) 
 ┬ ║   ║ ║  ║  ║   - 2593.965 - 0x7f73ff459780(0) old 
 └╦╝   ║ ║  ║  ║   - 3154.991 - 0x7f73ff459a20(0) 
  ║    ║ ╚╦═╝  ║   - 3561.681 - 0x7f73ff4592b0(0) 
  ║  ┬ ║  ║    ║   - 4391.037 - 0x7f73ff4596a0(0) old 
  ║  └╦╝  ║    ║   - 5540.058 - 0x7f73ff459550(0) 
  ║   ║   ║    ║ ┬ - 7830.847 - 0x7f73ff459470(0) old 
  ╚═╦═╝   ║    ║ │ - 7968.794 - 0x7f73ff4598d0(0) 
    ║     ║    ╚╦┘ - 21088.22 - 0x7f73ff4594e0(0) 
    ╚═══╦═╝     ║  - 23589.55 - 0x7f73ff4599b0(0) 
        ╚═════╦═╝  - 25766.77 - 0x7f73ff459630(0) 
┬                  - 45737.77 - 0x7f73ff4597f0(0)

whose tree string is (((1:0.19922,5:0.19922):0.390519,(2:0.089042,(3:0.00674687,6:0.00674687):0.0822952):0.500697):0.0544305,4:0.644169);

after the recombination, the tree has become

  ╦   ╦ ╦ ╦ ╦   ╦   -       0 - 1:0x7f73ff459010(0) 5:0x7f73ff459320(0) 2:0x7f73ff459080(0) 3:0x7f73ff459160(0) 6:0x7f73ff459400(0) 4:0x7f73ff459240(0) 
  ║   ║ ║ ╚╦╝   ║   - 269.8746 - 0x7f73ff459860(0) 
┬ ║   ║ ║  ║    ║   - 2593.965 - 0x7f73ff459780(0) old 
└╦╝   ║ ║  ║    ║   - 3154.991 - 0x7f73ff459a20(0) 
 ║    ║ ╚╦═╝    ║   - 3561.681 - 0x7f73ff4592b0(0) 
 ║  ┬ ║  ║      ║   - 4391.037 - 0x7f73ff4596a0(0) old 
 ║  └╦╝  ║      ║   - 5540.058 - 0x7f73ff459550(0) 
 ║   ║   ║      ║ ┬ - 7830.847 - 0x7f73ff459470(0) old 
 ╚═╦═╝   ║      ║ │ - 7968.794 - 0x7f73ff4598d0(0) 
   ║     ║      ╚╦┘ - 21088.22 - 0x7f73ff4594e0(0) 
   ╚═══╦═╝       ║  - 23589.55 - 0x7f73ff4599b0(0) 
       ║      ┬  ║  - 24654.73 - 0x7f73ff4591d0(0) 
       ╚═════╦┘  ║  - 25766.77 - 0x7f73ff459630(0) 
             ╚═╦═╝  - 34233.59 - 0x7f73ff4590f0(0)

whose tree string is (((1:0.19922,5:0.19922):0.390519,(2:0.089042,(3:0.00674687,6:0.00674687):0.0822952):0.500697):0.266101,4:0.85584);

However, scrm calculate the segment length, and do not print out tree, whose length is no greater than 0. In our case, the last tree was not printed in scrm, but in smcsmcSCRM

shajoezhu commented 9 years ago

partially fixed, and made further...

but failed at a new check, see the following:

 ./check_smcsmcSCRM_vs_scrm.sh 
Testing smcsmcSCRM 
 smcsmcSCRM -nsam 2 -Np 1 -r 130 1000000 ..........
 smcsmcSCRM -nsam 3 -Np 1 -r 130 1000000 ..........
 smcsmcSCRM -nsam 4 -Np 1 -r 130 1000000 ..........
 smcsmcSCRM -nsam 5 -Np 1 -r 130 1000000 ..........
 smcsmcSCRM -nsam 6 -Np 1 -r 130 1000000 ..........
 smcsmcSCRM -nsam 7 -Np 1 -r 130 1000000 ..........
 smcsmcSCRM -nsam 8 -Np 1 -r 130 1000000 ..........
 smcsmcSCRM -nsam 9 -Np 1 -r 130 1000000 ..........
 smcsmcSCRM -nsam 10 -Np 1 -r 130 1000000 ........1c1
< (((4:0.0273824,(5:0.016188,3:0.016188):0.0111944):0.357509,((7:0.0409916,1:0.0409916):0.188202,(8:0.170867,2:0.170867):0.0583261):0.155699):1.40193,(6:0.100553,(10:0.0490224,9:0.0490224):0.0515309):1.68627);
---
> ((8:0.0585906,9:0.0585906):0.369212,((4:0.0273824,(5:0.016188,(3:0.0140947,10:0.0140947):0.00209328):0.0111944):0.393702,(2:0.314867,((7:0.0159708,1:0.0159708):0.234753,6:0.250724):0.0641428):0.106218):0.00671817);

Failed at random seed:  8
Testing for Last tree in scrm and smcsmc.
../scrm  10 1 -r 130 1000000 -T -l 0 -seed 8
../smcsmcSCRM  -nsam 10 -Np 1 -r 130 1000000 -seed 8
joezhu@joezhu-M3800:~/smcsmcPerformance/smcsmc/tests$ wc scrm_tmp_tree smcsmc_tmp_tree 
   324    324  68455 scrm_tmp_tree
   322    322  68056 smcsmc_tmp_tree
   646    646 136511 total
joezhu@joezhu-M3800:~/smcsmcPerformance/smcsmc/tests$ diff scrm_tmp_tree smcsmc_tmp_tree 
311,324c311,322
< (2:0.444921,((1:0.23891,((7:0.0384285,6:0.0384285):0.0621248,(8:0.0585906,9:0.0585906):0.0419626):0.138356):0.188893,(4:0.0273824,(5:0.016188,(3:0.0140947,10:0.0140947):0.00209328):0.0111944):0.40042):0.017118);
< (2:0.444921,((1:0.23891,(6:0.100553,(8:0.0585906,(7:0.0490224,9:0.0490224):0.00956822):0.0419626):0.138356):0.188893,(4:0.0273824,(5:0.016188,(3:0.0140947,10:0.0140947):0.00209328):0.0111944):0.40042):0.017118);
< ((1:0.384892,2:0.384892):0.060029,((6:0.100553,(8:0.0585906,(7:0.0490224,9:0.0490224):0.00956822):0.0419626):0.32725,(4:0.0273824,(5:0.016188,(3:0.0140947,10:0.0140947):0.00209328):0.0111944):0.40042):0.017118);
< ((1:0.384892,(8:0.170867,2:0.170867):0.214025):0.060029,((6:0.100553,(7:0.0490224,9:0.0490224):0.0515309):0.32725,(4:0.0273824,(5:0.016188,(3:0.0140947,10:0.0140947):0.00209328):0.0111944):0.40042):0.017118);
< (((1:0.384892,(8:0.170867,2:0.170867):0.214025):0.060029,(4:0.0273824,(5:0.016188,(3:0.0140947,10:0.0140947):0.00209328):0.0111944):0.417538):0.265925,(6:0.100553,(7:0.0490224,9:0.0490224):0.0515309):0.610293);
< ((((4:0.0273824,(5:0.016188,(3:0.0140947,10:0.0140947):0.00209328):0.0111944):0.263268,1:0.29065):0.0942415,(8:0.170867,2:0.170867):0.214025):0.325954,(6:0.100553,(7:0.0490224,9:0.0490224):0.0515309):0.610293);
< ((((4:0.0273824,(5:0.016188,3:0.016188):0.0111944):0.263268,1:0.29065):0.0942415,(8:0.170867,2:0.170867):0.214025):0.325954,(6:0.100553,((10:0.0478433,7:0.0478433):0.00117911,9:0.0490224):0.0515309):0.610293);
< ((((4:0.0273824,(5:0.016188,3:0.016188):0.0111944):0.263268,1:0.29065):0.0942415,(8:0.170867,2:0.170867):0.214025):0.325954,(6:0.100553,((10:0.0478433,7:0.0478433):0.00117911,9:0.0490224):0.0515309):0.610293);
< ((((4:0.0273824,(5:0.016188,3:0.016188):0.0111944):0.263268,1:0.29065):0.0942415,(8:0.170867,2:0.170867):0.214025):0.325954,(6:0.100553,((10:0.0478433,7:0.0478433):0.00117911,9:0.0490224):0.0515309):0.610293);
< ((((4:0.0273824,(5:0.016188,3:0.016188):0.0111944):0.263268,(7:0.0409916,1:0.0409916):0.249659):0.0942415,(8:0.170867,2:0.170867):0.214025):0.325954,(6:0.100553,(10:0.0490224,9:0.0490224):0.0515309):0.610293);
< (((4:0.0273824,(5:0.016188,3:0.016188):0.0111944):0.357509,((7:0.0409916,1:0.0409916):0.188202,(8:0.170867,2:0.170867):0.0583261):0.155699):0.325954,(6:0.100553,(10:0.0490224,9:0.0490224):0.0515309):0.610293);
< ((6:0.100553,(10:0.0490224,9:0.0490224):0.0515309):0.874169,((4:0.0273824,(5:0.016188,3:0.016188):0.0111944):0.357509,((7:0.0409916,1:0.0409916):0.188202,(8:0.170867,2:0.170867):0.0583261):0.155699):0.589831);
< ((6:0.100553,(10:0.0490224,9:0.0490224):0.0515309):0.874169,((4:0.0273824,(5:0.016188,3:0.016188):0.0111944):0.357509,((7:0.0409916,1:0.0409916):0.188202,(8:0.170867,2:0.170867):0.0583261):0.155699):0.589831);
< (((4:0.0273824,(5:0.016188,3:0.016188):0.0111944):0.357509,((7:0.0409916,1:0.0409916):0.188202,(8:0.170867,2:0.170867):0.0583261):0.155699):1.40193,(6:0.100553,(10:0.0490224,9:0.0490224):0.0515309):1.68627);
---
> (((1:0.23891,((7:0.0384285,6:0.0384285):0.0621248,(8:0.0585906,9:0.0585906):0.0419626):0.138356):0.188893,2:0.427803):0.017118,(4:0.0273824,(5:0.016188,(3:0.0140947,10:0.0140947):0.00209328):0.0111944):0.417538);
> (((1:0.23891,((7:0.0384285,6:0.0384285):0.0621248,(8:0.0585906,9:0.0585906):0.0419626):0.138356):0.188893,2:0.427803):0.017118,(4:0.0273824,(5:0.016188,(3:0.0140947,10:0.0140947):0.00209328):0.0111944):0.417538);
> (((1:0.23891,(6:0.100553,(8:0.0585906,9:0.0585906):0.0419626):0.138356):0.188893,(7:0.378465,2:0.378465):0.0493382):0.017118,(4:0.0273824,(5:0.016188,(3:0.0140947,10:0.0140947):0.00209328):0.0111944):0.417538);
> (((1:0.23891,(6:0.100553,(8:0.0585906,9:0.0585906):0.0419626):0.138356):0.188893,7:0.427803):0.017118,(2:0.361424,(4:0.0273824,(5:0.016188,(3:0.0140947,10:0.0140947):0.00209328):0.0111944):0.334041):0.0834971);
> (((1:0.23891,(6:0.100553,(8:0.0585906,9:0.0585906):0.0419626):0.138356):0.188893,7:0.427803):0.408397,(2:0.361424,(4:0.0273824,(5:0.016188,(3:0.0140947,10:0.0140947):0.00209328):0.0111944):0.334041):0.474776);
> ((1:0.23891,(6:0.100553,(8:0.0585906,9:0.0585906):0.0419626):0.138356):0.188893,((2:0.361424,(4:0.0273824,(5:0.016188,(3:0.0140947,10:0.0140947):0.00209328):0.0111944):0.334041):0.059661,7:0.421085):0.00671817);
> ((1:0.23891,(8:0.0585906,9:0.0585906):0.180319):0.188893,((2:0.361424,(4:0.0273824,(5:0.016188,(3:0.0140947,10:0.0140947):0.00209328):0.0111944):0.334041):0.059661,(6:0.062108,7:0.062108):0.358977):0.00671817);
> ((8:0.0585906,9:0.0585906):0.369212,((2:0.361424,(4:0.0273824,(5:0.016188,(3:0.0140947,10:0.0140947):0.00209328):0.0111944):0.334041):0.059661,(1:0.250724,(6:0.062108,7:0.062108):0.188616):0.17036):0.00671817);
> ((8:0.0585906,9:0.0585906):0.369212,((2:0.361424,(4:0.0273824,(5:0.016188,(3:0.0140947,10:0.0140947):0.00209328):0.0111944):0.334041):0.059661,(1:0.250724,(6:0.062108,7:0.062108):0.188616):0.17036):0.00671817);
> ((8:0.0585906,9:0.0585906):0.369212,((2:0.361424,(4:0.0273824,(5:0.016188,(3:0.0140947,10:0.0140947):0.00209328):0.0111944):0.334041):0.059661,((7:0.0159708,1:0.0159708):0.234753,6:0.250724):0.17036):0.00671817);
> ((8:0.0585906,9:0.0585906):0.369212,((4:0.0273824,(5:0.016188,(3:0.0140947,10:0.0140947):0.00209328):0.0111944):0.393702,(2:0.314867,((7:0.0159708,1:0.0159708):0.234753,6:0.250724):0.0641428):0.106218):0.00671817);
> ((8:0.0585906,9:0.0585906):0.369212,((4:0.0273824,(5:0.016188,(3:0.0140947,10:0.0140947):0.00209328):0.0111944):0.393702,(2:0.314867,((7:0.0159708,1:0.0159708):0.234753,6:0.250724):0.0641428):0.106218):0.00671817);
shajoezhu commented 9 years ago

At segment 311, not sure if something went wrong at the recording step. all the node height are the same, but coalescent seems to be implemented onto different branches ...

scrm debug output

===== BUILDING NEXT GENEALOGY =====
        scrm Segment Nr: 311 | Sequence position: 945810.4
╦   ╦ ╦ ╦ ╦   ╦ ╦ ╦ ╦ ╦ -       0 - 1:0x7f919ea87010(0) 7:0x7f919ea874e0(0) 6:0x7f919ea87400(0) 8:0x7f919ea875c0(0) 9:0x7f919ea876a0(0) 2:0x7f919ea87080(0) 4:0x7f919ea87240(0
) 5:0x7f919ea87320(0) 3:0x7f919ea87160(0) 10:0x7f919ea87780(0) 
║   ║ ║ ║ ║   ║ ║ ║ ╚╦╝ - 563.7877 - 0x7f919ea878d0(0) 
║   ║ ║ ║ ║   ║ ║ ╚╦═╝  - 647.5188 - 0x7f919ea87e80(0) 
║ ┬ ║ ║ ║ ║   ║ ║  ║    - 716.3593 - 0x7f919ea87390(0) old 
║ │ ║ ║ ║ ║   ║ ╚╦═╝    - 1095.296 - 0x7f919ea87550(0) 
║ └╦╝ ║ ║ ║   ║  ║      - 1308.836 - 0x7f919ea87da0(0) 
║  ╚═╦╝ ║ ║   ║  ║      - 1537.139 - 0x7f919ea87cc0(0) 
║    ║  ╚╦╝   ║  ║      - 2343.626 - 0x7f919ea87710(0) 
║    ╚═╦═╝    ║  ║      - 4022.131 - 0x7f919ea87c50(0) 
║      ║    ┬ ║  ║      - 7255.582 - 0x7f919ea870f0(0) old 
╚╦═════╝    │ ║  ║      - 9556.383 - 0x7f919ea87860(0) 
 ╚═════════╦┘ ║  ║      - 13236.71 - 0x7f919ea87e10(0) 
           ║  ╚╦═╝      - 17796.83 - 0x7f919ea87be0(0) 
           ╚═╦═╝        - 25882.26 - 0x7f919ea87470(0) 
        scrm * Recombination at height 11723.55 (above 0x7f919ea87860)
        scrm * Cutting subtree below recombination 
        scrm * * New leaf of local tree: 0x7f919ea87a20
        scrm * * New root of subtree: 0x7f919ea87b00
        scrm * * Done
    ╦ ╦ ╦ ╦ ╦╦   ╦ ╦ ╦ ╦  -       0 - 2:0x7f919ea87080(0) 4:0x7f919ea87240(0) 5:0x7f919ea87320(0) 3:0x7f919ea87160(0) 10:0x7f919ea87780(0) 1:0x7f919ea87010(0) 7:0x7f919ea874e
0(0) 6:0x7f919ea87400(0) 8:0x7f919ea875c0(0) 9:0x7f919ea876a0(0) 
    ║ ║ ║ ╚╦╝║   ║ ║ ║ ║  - 563.7877 - 0x7f919ea878d0(0) 
    ║ ║ ╚╦═╝ ║   ║ ║ ║ ║  - 647.5188 - 0x7f919ea87e80(0) 
    ║ ║  ║   ║ ┬ ║ ║ ║ ║  - 716.3593 - 0x7f919ea87390(0) old 
    ║ ╚╦═╝   ║ │ ║ ║ ║ ║  - 1095.296 - 0x7f919ea87550(0) 
    ║  ║     ║ └╦╝ ║ ║ ║  - 1308.836 - 0x7f919ea87da0(0) 
    ║  ║     ║  ╚═╦╝ ║ ║  - 1537.139 - 0x7f919ea87cc0(0) 
    ║  ║     ║    ║  ╚╦╝  - 2343.626 - 0x7f919ea87710(0) 
    ║  ║     ║    ╚═╦═╝   - 4022.131 - 0x7f919ea87c50(0) 
  ┬ ║  ║     ║      ║     - 7255.582 - 0x7f919ea870f0(0) old 
  │ ║  ║     ╚╦═════╝     - 9556.383 - 0x7f919ea87860(0) 
┬ │ ║  ║      ╚═════════╦ - 11723.55 - 0x7f919ea87a20(0) 0x7f919ea87b00(0) 
└┬┘ ║  ║                  - 13236.71 - 0x7f919ea87e10(0) 
 │  ╚╦═╝                  - 17796.83 - 0x7f919ea87be0(0) 
 └─╦═╝                    - 25882.26 - 0x7f919ea87470(0) 
        scrm * Starting coalescence
        scrm * * * PRUNING: Removing branch above 0x7f919ea870f0 from tree (old)
        scrm * * * PRUNING: Removing node 0x7f919ea87e10 from tree (unneeded)
        scrm * * Time interval: 11723.55 - 17796.83 (Last event at 11723.55)
        scrm * * * Active Nodes: a0:0x7f919ea87b00:s1(p0) a1:0x7f919ea87470:s0(p0)
        scrm * * * Total Rates: 0.00015 0 0
        scrm * * * Event at time 17112.11: Coalesence of a0
        scrm * * * Above node 0x7f919ea87550
        scrm * * * We hit the local tree. Done.
  ╦ ╦   ╦ ╦ ╦ ╦ ╦ ╦ ╦ ╦ -       0 - 2:0x7f919ea87080(0) 1:0x7f919ea87010(0) 7:0x7f919ea874e0(0) 6:0x7f919ea87400(0) 8:0x7f919ea875c0(0) 9:0x7f919ea876a0(0) 4:0x7f919ea87240(0) 5:0x7f919ea87320(0) 3:0x7f919ea87160(0) 10:0x7f919ea87780(0) 
  ║ ║   ║ ║ ║ ║ ║ ║ ╚╦╝ - 563.7877 - 0x7f919ea878d0(0) 
  ║ ║   ║ ║ ║ ║ ║ ╚╦═╝  - 647.5188 - 0x7f919ea87e80(0) 
  ║ ║ ┬ ║ ║ ║ ║ ║  ║    - 716.3593 - 0x7f919ea87390(0) old 
  ║ ║ │ ║ ║ ║ ║ ╚╦═╝    - 1095.296 - 0x7f919ea87550(0) 
  ║ ║ └╦╝ ║ ║ ║  ║      - 1308.836 - 0x7f919ea87da0(0) 
  ║ ║  ╚═╦╝ ║ ║  ║      - 1537.139 - 0x7f919ea87cc0(0) 
  ║ ║    ║  ╚╦╝  ║      - 2343.626 - 0x7f919ea87710(0) 
  ║ ║    ╚═╦═╝   ║      - 4022.131 - 0x7f919ea87c50(0) 
  ║ ╚╦═════╝     ║      - 9556.383 - 0x7f919ea87860(0) 
┬ ║  ║           ║      - 11723.55 - 0x7f919ea87a20(0) 
│ ║  ╚═════════╦═╝      - 17112.11 - 0x7f919ea87b00(0) 
│ ╚╦═══════════╝        - 17796.83 - 0x7f919ea87be0(0) 
└┬─┘                    - 25882.26 - 0x7f919ea87470(0) 
  ╦ ╦   ╦ ╦ ╦ ╦ ╦ ╦ ╦ ╦ -       0 - 2:0x7f919ea87080(0) 1:0x7f919ea87010(0) 7:0x7f919ea874e0(0) 6:0x7f919ea87400(0) 8:0x7f919ea875c0(0) 9:0x7f919ea876a0(0) 4:0x7f919ea87240(0) 5:0x7f919ea87320(0) 3:0x7f919ea87160(0) 10:0x7f919ea87780(0) 
  ║ ║   ║ ║ ║ ║ ║ ║ ╚╦╝ - 563.7877 - 0x7f919ea878d0(0) 
  ║ ║   ║ ║ ║ ║ ║ ╚╦═╝  - 647.5188 - 0x7f919ea87e80(0) 
  ║ ║ ┬ ║ ║ ║ ║ ║  ║    - 716.3593 - 0x7f919ea87390(0) old 
  ║ ║ │ ║ ║ ║ ║ ╚╦═╝    - 1095.296 - 0x7f919ea87550(0) 
  ║ ║ └╦╝ ║ ║ ║  ║      - 1308.836 - 0x7f919ea87da0(0) 
  ║ ║  ╚═╦╝ ║ ║  ║      - 1537.139 - 0x7f919ea87cc0(0) 
  ║ ║    ║  ╚╦╝  ║      - 2343.626 - 0x7f919ea87710(0) 
  ║ ║    ╚═╦═╝   ║      - 4022.131 - 0x7f919ea87c50(0) 
  ║ ╚╦═════╝     ║      - 9556.383 - 0x7f919ea87860(0) 
┬ ║  ║           ║      - 11723.55 - 0x7f919ea87a20(0) 
│ ║  ╚═════════╦═╝      - 17112.11 - 0x7f919ea87b00(0) 
│ ╚╦═══════════╝        - 17796.83 - 0x7f919ea87be0(0) 
└┬─┘                    - 25882.26 - 0x7f919ea87470(0)

smcsmc output

        scrm Segment Nr: 311 | Sequence position: 945810.4
╦   ╦ ╦ ╦ ╦   ╦ ╦ ╦ ╦ ╦ -       0 - 1:0x7fc115ac3010(0) 7:0x7fc115ac34e0(0) 6:0x7fc115ac3400(0) 8:0x7fc115ac35c0(0) 9:0x7fc115ac36a0(0) 2:0x7fc115ac3080(0) 4:0x7fc115ac3240(0
) 5:0x7fc115ac3320(0) 3:0x7fc115ac3160(0) 10:0x7fc115ac3780(0) 
║   ║ ║ ║ ║   ║ ║ ║ ╚╦╝ - 563.7877 - 0x7fc115ac38d0(0) 
║   ║ ║ ║ ║   ║ ║ ╚╦═╝  - 647.5188 - 0x7fc115ac3e80(0) 
║ ┬ ║ ║ ║ ║   ║ ║  ║    - 716.3593 - 0x7fc115ac3390(0) old 
║ │ ║ ║ ║ ║   ║ ╚╦═╝    - 1095.296 - 0x7fc115ac3550(0) 
║ └╦╝ ║ ║ ║   ║  ║      - 1308.836 - 0x7fc115ac3da0(0) 
║  ╚═╦╝ ║ ║   ║  ║      - 1537.139 - 0x7fc115ac3cc0(0) 
║    ║  ╚╦╝   ║  ║      - 2343.626 - 0x7fc115ac3710(0) 
║    ╚═╦═╝    ║  ║      - 4022.131 - 0x7fc115ac3c50(0) 
║      ║    ┬ ║  ║      - 7255.582 - 0x7fc115ac30f0(0) old 
╚╦═════╝    │ ║  ║      - 9556.383 - 0x7fc115ac3860(0) 
 ╚═════════╦┘ ║  ║      - 13236.71 - 0x7fc115ac3e10(0) 
           ║  ╚╦═╝      - 17796.83 - 0x7fc115ac3be0(0) 
           ╚═╦═╝        - 25882.26 - 0x7fc115ac3470(0) 
        scrm * Recombination at height 11723.55 (above 0x7fc115ac3860)
        scrm * Cutting subtree below recombination 
        scrm * * New leaf of local tree: 0x7fc115ac3a20
        scrm * * New root of subtree: 0x7fc115ac3b00
        scrm * * Done
    ╦ ╦ ╦ ╦ ╦╦   ╦ ╦ ╦ ╦  -       0 - 2:0x7fc115ac3080(0) 4:0x7fc115ac3240(0) 5:0x7fc115ac3320(0) 3:0x7fc115ac3160(0) 10:0x7fc115ac3780(0) 1:0x7fc115ac3010(0) 7:0x7fc115ac34e
0(0) 6:0x7fc115ac3400(0) 8:0x7fc115ac35c0(0) 9:0x7fc115ac36a0(0) 
    ║ ║ ║ ╚╦╝║   ║ ║ ║ ║  - 563.7877 - 0x7fc115ac38d0(0) 
    ║ ║ ╚╦═╝ ║   ║ ║ ║ ║  - 647.5188 - 0x7fc115ac3e80(0) 
    ║ ║  ║   ║ ┬ ║ ║ ║ ║  - 716.3593 - 0x7fc115ac3390(0) old 
    ║ ╚╦═╝   ║ │ ║ ║ ║ ║  - 1095.296 - 0x7fc115ac3550(0) 
    ║  ║     ║ └╦╝ ║ ║ ║  - 1308.836 - 0x7fc115ac3da0(0) 
    ║  ║     ║  ╚═╦╝ ║ ║  - 1537.139 - 0x7fc115ac3cc0(0) 
    ║  ║     ║    ║  ╚╦╝  - 2343.626 - 0x7fc115ac3710(0) 
    ║  ║     ║    ╚═╦═╝   - 4022.131 - 0x7fc115ac3c50(0) 
  ┬ ║  ║     ║      ║     - 7255.582 - 0x7fc115ac30f0(0) old 
  │ ║  ║     ╚╦═════╝     - 9556.383 - 0x7fc115ac3860(0) 
┬ │ ║  ║      ╚═════════╦ - 11723.55 - 0x7fc115ac3a20(0) 0x7fc115ac3b00(0) 
└┬┘ ║  ║                  - 13236.71 - 0x7fc115ac3e10(0) 
 │  ╚╦═╝                  - 17796.83 - 0x7fc115ac3be0(0) 
 └─╦═╝                    - 25882.26 - 0x7fc115ac3470(0) 
        scrm * Starting coalescence
        scrm * * * PRUNING: Removing branch above 0x7fc115ac30f0 from tree (old)
        scrm * * * PRUNING: Removing node 0x7fc115ac3e10 from tree (unneeded)
        scrm * * Time interval: 11723.55 - 17796.83 (Last event at 11723.55)
        scrm * * * Active Nodes: a0:0x7fc115ac3b00:s1(p0) a1:0x7fc115ac3470:s0(p0)
        scrm * * * Total Rates: 0.00015 0 0
        scrm * * * Event at time 17112.11: Coalesence of a0
    ForestState Start Recording 
    ForestState     EventRecorder Event CoalMigr w=3 [945810.4] pop=0 t=11723.55-17112.11 (**COAL**) 
    ForestState Finish recording of event.
        scrm * * * Above node 0x7fc115ac3080
        scrm * * * We hit the local tree. Done.
  ╦   ╦ ╦ ╦ ╦ ╦ ╦ ╦ ╦ ╦ -       0 - 1:0x7fc115ac3010(0) 7:0x7fc115ac34e0(0) 6:0x7fc115ac3400(0) 8:0x7fc115ac35c0(0) 9:0x7fc115ac36a0(0) 2:0x7fc115ac3080(0) 4:0x7fc115ac3240(0) 5:0x7fc115ac3320(0) 3:0x7fc115ac3160(0) 10:0x7fc115ac3780(0) 
  ║   ║ ║ ║ ║ ║ ║ ║ ╚╦╝ - 563.7877 - 0x7fc115ac38d0(0) 
  ║   ║ ║ ║ ║ ║ ║ ╚╦═╝  - 647.5188 - 0x7fc115ac3e80(0) 
  ║ ┬ ║ ║ ║ ║ ║ ║  ║    - 716.3593 - 0x7fc115ac3390(0) old 
  ║ │ ║ ║ ║ ║ ║ ╚╦═╝    - 1095.296 - 0x7fc115ac3550(0) 
  ║ └╦╝ ║ ║ ║ ║  ║      - 1308.836 - 0x7fc115ac3da0(0) 
  ║  ╚═╦╝ ║ ║ ║  ║      - 1537.139 - 0x7fc115ac3cc0(0) 
  ║    ║  ╚╦╝ ║  ║      - 2343.626 - 0x7fc115ac3710(0) 
  ║    ╚═╦═╝  ║  ║      - 4022.131 - 0x7fc115ac3c50(0) 
  ╚╦═════╝    ║  ║      - 9556.383 - 0x7fc115ac3860(0) 
┬  ║          ║  ║      - 11723.55 - 0x7fc115ac3a20(0) 
│  ╚═════════╦╝  ║      - 17112.11 - 0x7fc115ac3b00(0) 
│            ╚═╦═╝      - 17796.83 - 0x7fc115ac3be0(0) 
└┬─────────────┘        - 25882.26 - 0x7fc115ac3470(0) 
  ╦   ╦ ╦ ╦ ╦ ╦ ╦ ╦ ╦ ╦ -       0 - 1:0x7fc115ac3010(0) 7:0x7fc115ac34e0(0) 6:0x7fc115ac3400(0) 8:0x7fc115ac35c0(0) 9:0x7fc115ac36a0(0) 2:0x7fc115ac3080(0) 4:0x7fc115ac3240(0) 5:0x7fc115ac3320(0) 3:0x7fc115ac3160(0) 10:0x7fc115ac3780(0) 
  ║   ║ ║ ║ ║ ║ ║ ║ ╚╦╝ - 563.7877 - 0x7fc115ac38d0(0) 
  ║   ║ ║ ║ ║ ║ ║ ╚╦═╝  - 647.5188 - 0x7fc115ac3e80(0) 
  ║ ┬ ║ ║ ║ ║ ║ ║  ║    - 716.3593 - 0x7fc115ac3390(0) old 
  ║ │ ║ ║ ║ ║ ║ ╚╦═╝    - 1095.296 - 0x7fc115ac3550(0) 
  ║ └╦╝ ║ ║ ║ ║  ║      - 1308.836 - 0x7fc115ac3da0(0) 
  ║  ╚═╦╝ ║ ║ ║  ║      - 1537.139 - 0x7fc115ac3cc0(0) 
  ║    ║  ╚╦╝ ║  ║      - 2343.626 - 0x7fc115ac3710(0) 
  ║    ╚═╦═╝  ║  ║      - 4022.131 - 0x7fc115ac3c50(0) 
  ╚╦═════╝    ║  ║      - 9556.383 - 0x7fc115ac3860(0) 
┬  ║          ║  ║      - 11723.55 - 0x7fc115ac3a20(0) 
│  ╚═════════╦╝  ║      - 17112.11 - 0x7fc115ac3b00(0) 
│            ╚═╦═╝      - 17796.83 - 0x7fc115ac3be0(0) 
└┬─────────────┘        - 25882.26 - 0x7fc115ac3470(0)
shajoezhu commented 9 years ago

As a result, we have the following trees, scrm coalesced the two big clades, then external node 2, smcsmc coalesced external node 2 with one of the clades first.

scrm: scrm

smcsmc: smcsmc

gerton commented 9 years ago

I wonder, is the ordering of the contemporaries guaranteed to be the same every time? If for instance their order depends on their location in memory, you would get differences, but they would not be problematic.

If you suspect that this may be the case, one potential way to check is to temporarily guarantee an order on the basis of something that is guaranteed to be unique per node. You could draw a random number and put it in the data structure, and order by that — with the same random number generator this would guarantee an identical ordering.

Just a thought…

BW G

On 22 Oct 2015, at 16:20, Joe Zhu notifications@github.com wrote:

At segment 311, not sure if something went wrong at the recording step. all the node height are the same, but coalescent seems to be implemented onto different branches ...

scrm debug output

===== BUILDING NEXT GENEALOGY ===== scrm Segment Nr: 311 | Sequence position: 945810.4 ╦ ╦ ╦ ╦ ╦ ╦ ╦ ╦ ╦ ╦ - 0 - 1:0x7f919ea87010(0) 7:0x7f919ea874e0(0) 6:0x7f919ea87400(0) 8:0x7f919ea875c0(0) 9:0x7f919ea876a0(0) 2:0x7f919ea87080(0) 4:0x7f919ea87240(0 ) 5:0x7f919ea87320(0) 3:0x7f919ea87160(0) 10:0x7f919ea87780(0) ║ ║ ║ ║ ║ ║ ║ ║ ╚╦╝ - 563.7877 - 0x7f919ea878d0(0) ║ ║ ║ ║ ║ ║ ║ ╚╦═╝ - 647.5188 - 0x7f919ea87e80(0) ║ ┬ ║ ║ ║ ║ ║ ║ ║ - 716.3593 - 0x7f919ea87390(0) old ║ │ ║ ║ ║ ║ ║ ╚╦═╝ - 1095.296 - 0x7f919ea87550(0) ║ └╦╝ ║ ║ ║ ║ ║ - 1308.836 - 0x7f919ea87da0(0) ║ ╚═╦╝ ║ ║ ║ ║ - 1537.139 - 0x7f919ea87cc0(0) ║ ║ ╚╦╝ ║ ║ - 2343.626 - 0x7f919ea87710(0) ║ ╚═╦═╝ ║ ║ - 4022.131 - 0x7f919ea87c50(0) ║ ║ ┬ ║ ║ - 7255.582 - 0x7f919ea870f0(0) old ╚╦═════╝ │ ║ ║ - 9556.383 - 0x7f919ea87860(0) ╚═════════╦┘ ║ ║ - 13236.71 - 0x7f919ea87e10(0) ║ ╚╦═╝ - 17796.83 - 0x7f919ea87be0(0) ╚═╦═╝ - 25882.26 - 0x7f919ea87470(0) scrm * Recombination at height 11723.55 (above 0x7f919ea87860) scrm * Cutting subtree below recombination scrm * * New leaf of local tree: 0x7f919ea87a20 scrm * * New root of subtree: 0x7f919ea87b00 scrm * * Done ╦ ╦ ╦ ╦ ╦╦ ╦ ╦ ╦ ╦ - 0 - 2:0x7f919ea87080(0) 4:0x7f919ea87240(0) 5:0x7f919ea87320(0) 3:0x7f919ea87160(0) 10:0x7f919ea87780(0) 1:0x7f919ea87010(0) 7:0x7f919ea874e 0(0) 6:0x7f919ea87400(0) 8:0x7f919ea875c0(0) 9:0x7f919ea876a0(0) ║ ║ ║ ╚╦╝║ ║ ║ ║ ║ - 563.7877 - 0x7f919ea878d0(0) ║ ║ ╚╦═╝ ║ ║ ║ ║ ║ - 647.5188 - 0x7f919ea87e80(0) ║ ║ ║ ║ ┬ ║ ║ ║ ║ - 716.3593 - 0x7f919ea87390(0) old ║ ╚╦═╝ ║ │ ║ ║ ║ ║ - 1095.296 - 0x7f919ea87550(0) ║ ║ ║ └╦╝ ║ ║ ║ - 1308.836 - 0x7f919ea87da0(0) ║ ║ ║ ╚═╦╝ ║ ║ - 1537.139 - 0x7f919ea87cc0(0) ║ ║ ║ ║ ╚╦╝ - 2343.626 - 0x7f919ea87710(0) ║ ║ ║ ╚═╦═╝ - 4022.131 - 0x7f919ea87c50(0) ┬ ║ ║ ║ ║ - 7255.582 - 0x7f919ea870f0(0) old │ ║ ║ ╚╦═════╝ - 9556.383 - 0x7f919ea87860(0) ┬ │ ║ ║ ╚═════════╦ - 11723.55 - 0x7f919ea87a20(0) 0x7f919ea87b00(0) └┬┘ ║ ║ - 13236.71 - 0x7f919ea87e10(0) │ ╚╦═╝ - 17796.83 - 0x7f919ea87be0(0) └─╦═╝ - 25882.26 - 0x7f919ea87470(0) scrm * Starting coalescence scrm * * * PRUNING: Removing branch above 0x7f919ea870f0 from tree (old) scrm * * * PRUNING: Removing node 0x7f919ea87e10 from tree (unneeded) scrm * * Time interval: 11723.55 - 17796.83 (Last event at 11723.55) scrm * * * Active Nodes: a0:0x7f919ea87b00:s1(p0) a1:0x7f919ea87470:s0(p0) scrm * * * Total Rates: 0.00015 0 0 scrm * * * Event at time 17112.11: Coalesence of a0 scrm * * * Above node 0x7f919ea87550 scrm * * * We hit the local tree. Done. ╦ ╦ ╦ ╦ ╦ ╦ ╦ ╦ ╦ ╦ - 0 - 2:0x7f919ea87080(0) 1:0x7f919ea87010(0) 7:0x7f919ea874e0(0) 6:0x7f919ea87400(0) 8:0x7f919ea875c0(0) 9:0x7f919ea876a0(0) 4:0x7f919ea87240(0) 5:0x7f919ea87320(0) 3:0x7f919ea87160(0) 10:0x7f919ea87780(0) ║ ║ ║ ║ ║ ║ ║ ║ ╚╦╝ - 563.7877 - 0x7f919ea878d0(0) ║ ║ ║ ║ ║ ║ ║ ╚╦═╝ - 647.5188 - 0x7f919ea87e80(0) ║ ║ ┬ ║ ║ ║ ║ ║ ║ - 716.3593 - 0x7f919ea87390(0) old ║ ║ │ ║ ║ ║ ║ ╚╦═╝ - 1095.296 - 0x7f919ea87550(0) ║ ║ └╦╝ ║ ║ ║ ║ - 1308.836 - 0x7f919ea87da0(0) ║ ║ ╚═╦╝ ║ ║ ║ - 1537.139 - 0x7f919ea87cc0(0) ║ ║ ║ ╚╦╝ ║ - 2343.626 - 0x7f919ea87710(0) ║ ║ ╚═╦═╝ ║ - 4022.131 - 0x7f919ea87c50(0) ║ ╚╦═════╝ ║ - 9556.383 - 0x7f919ea87860(0) ┬ ║ ║ ║ - 11723.55 - 0x7f919ea87a20(0) │ ║ ╚═════════╦═╝ - 17112.11 - 0x7f919ea87b00(0) │ ╚╦═══════════╝ - 17796.83 - 0x7f919ea87be0(0) └┬─┘ - 25882.26 - 0x7f919ea87470(0) ╦ ╦ ╦ ╦ ╦ ╦ ╦ ╦ ╦ ╦ - 0 - 2:0x7f919ea87080(0) 1:0x7f919ea87010(0) 7:0x7f919ea874e0(0) 6:0x7f919ea87400(0) 8:0x7f919ea875c0(0) 9:0x7f919ea876a0(0) 4:0x7f919ea87240(0) 5:0x7f919ea87320(0) 3:0x7f919ea87160(0) 10:0x7f919ea87780(0) ║ ║ ║ ║ ║ ║ ║ ║ ╚╦╝ - 563.7877 - 0x7f919ea878d0(0) ║ ║ ║ ║ ║ ║ ║ ╚╦═╝ - 647.5188 - 0x7f919ea87e80(0) ║ ║ ┬ ║ ║ ║ ║ ║ ║ - 716.3593 - 0x7f919ea87390(0) old ║ ║ │ ║ ║ ║ ║ ╚╦═╝ - 1095.296 - 0x7f919ea87550(0) ║ ║ └╦╝ ║ ║ ║ ║ - 1308.836 - 0x7f919ea87da0(0) ║ ║ ╚═╦╝ ║ ║ ║ - 1537.139 - 0x7f919ea87cc0(0) ║ ║ ║ ╚╦╝ ║ - 2343.626 - 0x7f919ea87710(0) ║ ║ ╚═╦═╝ ║ - 4022.131 - 0x7f919ea87c50(0) ║ ╚╦═════╝ ║ - 9556.383 - 0x7f919ea87860(0) ┬ ║ ║ ║ - 11723.55 - 0x7f919ea87a20(0) │ ║ ╚═════════╦═╝ - 17112.11 - 0x7f919ea87b00(0) │ ╚╦═══════════╝ - 17796.83 - 0x7f919ea87be0(0) └┬─┘ - 25882.26 - 0x7f919ea87470(0) smcsmc output

    scrm Segment Nr: 311 | Sequence position: 945810.4

╦ ╦ ╦ ╦ ╦ ╦ ╦ ╦ ╦ ╦ - 0 - 1:0x7fc115ac3010(0) 7:0x7fc115ac34e0(0) 6:0x7fc115ac3400(0) 8:0x7fc115ac35c0(0) 9:0x7fc115ac36a0(0) 2:0x7fc115ac3080(0) 4:0x7fc115ac3240(0 ) 5:0x7fc115ac3320(0) 3:0x7fc115ac3160(0) 10:0x7fc115ac3780(0) ║ ║ ║ ║ ║ ║ ║ ║ ╚╦╝ - 563.7877 - 0x7fc115ac38d0(0) ║ ║ ║ ║ ║ ║ ║ ╚╦═╝ - 647.5188 - 0x7fc115ac3e80(0) ║ ┬ ║ ║ ║ ║ ║ ║ ║ - 716.3593 - 0x7fc115ac3390(0) old ║ │ ║ ║ ║ ║ ║ ╚╦═╝ - 1095.296 - 0x7fc115ac3550(0) ║ └╦╝ ║ ║ ║ ║ ║ - 1308.836 - 0x7fc115ac3da0(0) ║ ╚═╦╝ ║ ║ ║ ║ - 1537.139 - 0x7fc115ac3cc0(0) ║ ║ ╚╦╝ ║ ║ - 2343.626 - 0x7fc115ac3710(0) ║ ╚═╦═╝ ║ ║ - 4022.131 - 0x7fc115ac3c50(0) ║ ║ ┬ ║ ║ - 7255.582 - 0x7fc115ac30f0(0) old ╚╦═════╝ │ ║ ║ - 9556.383 - 0x7fc115ac3860(0) ╚═════════╦┘ ║ ║ - 13236.71 - 0x7fc115ac3e10(0) ║ ╚╦═╝ - 17796.83 - 0x7fc115ac3be0(0) ╚═╦═╝ - 25882.26 - 0x7fc115ac3470(0) scrm * Recombination at height 11723.55 (above 0x7fc115ac3860) scrm * Cutting subtree below recombination scrm * * New leaf of local tree: 0x7fc115ac3a20 scrm * * New root of subtree: 0x7fc115ac3b00 scrm * * Done ╦ ╦ ╦ ╦ ╦╦ ╦ ╦ ╦ ╦ - 0 - 2:0x7fc115ac3080(0) 4:0x7fc115ac3240(0) 5:0x7fc115ac3320(0) 3:0x7fc115ac3160(0) 10:0x7fc115ac3780(0) 1:0x7fc115ac3010(0) 7:0x7fc115ac34e 0(0) 6:0x7fc115ac3400(0) 8:0x7fc115ac35c0(0) 9:0x7fc115ac36a0(0) ║ ║ ║ ╚╦╝║ ║ ║ ║ ║ - 563.7877 - 0x7fc115ac38d0(0) ║ ║ ╚╦═╝ ║ ║ ║ ║ ║ - 647.5188 - 0x7fc115ac3e80(0) ║ ║ ║ ║ ┬ ║ ║ ║ ║ - 716.3593 - 0x7fc115ac3390(0) old ║ ╚╦═╝ ║ │ ║ ║ ║ ║ - 1095.296 - 0x7fc115ac3550(0) ║ ║ ║ └╦╝ ║ ║ ║ - 1308.836 - 0x7fc115ac3da0(0) ║ ║ ║ ╚═╦╝ ║ ║ - 1537.139 - 0x7fc115ac3cc0(0) ║ ║ ║ ║ ╚╦╝ - 2343.626 - 0x7fc115ac3710(0) ║ ║ ║ ╚═╦═╝ - 4022.131 - 0x7fc115ac3c50(0) ┬ ║ ║ ║ ║ - 7255.582 - 0x7fc115ac30f0(0) old │ ║ ║ ╚╦═════╝ - 9556.383 - 0x7fc115ac3860(0) ┬ │ ║ ║ ╚═════════╦ - 11723.55 - 0x7fc115ac3a20(0) 0x7fc115ac3b00(0) └┬┘ ║ ║ - 13236.71 - 0x7fc115ac3e10(0) │ ╚╦═╝ - 17796.83 - 0x7fc115ac3be0(0) └─╦═╝ - 25882.26 - 0x7fc115ac3470(0) scrm * Starting coalescence scrm * * * PRUNING: Removing branch above 0x7fc115ac30f0 from tree (old) scrm * * * PRUNING: Removing node 0x7fc115ac3e10 from tree (unneeded) scrm * * Time interval: 11723.55 - 17796.83 (Last event at 11723.55) scrm * * * Active Nodes: a0:0x7fc115ac3b00:s1(p0) a1:0x7fc115ac3470:s0(p0) scrm * * * Total Rates: 0.00015 0 0 scrm * * * Event at time 17112.11: Coalesence of a0 ForestState Start Recording ForestState EventRecorder Event CoalMigr w=3 [945810.4] pop=0 t=11723.55-17112.11 (COAL) ForestState Finish recording of event. scrm * * * Above node 0x7fc115ac3080 scrm * * * We hit the local tree. Done. ╦ ╦ ╦ ╦ ╦ ╦ ╦ ╦ ╦ ╦ - 0 - 1:0x7fc115ac3010(0) 7:0x7fc115ac34e0(0) 6:0x7fc115ac3400(0) 8:0x7fc115ac35c0(0) 9:0x7fc115ac36a0(0) 2:0x7fc115ac3080(0) 4:0x7fc115ac3240(0) 5:0x7fc115ac3320(0) 3:0x7fc115ac3160(0) 10:0x7fc115ac3780(0) ║ ║ ║ ║ ║ ║ ║ ║ ╚╦╝ - 563.7877 - 0x7fc115ac38d0(0) ║ ║ ║ ║ ║ ║ ║ ╚╦═╝ - 647.5188 - 0x7fc115ac3e80(0) ║ ┬ ║ ║ ║ ║ ║ ║ ║ - 716.3593 - 0x7fc115ac3390(0) old ║ │ ║ ║ ║ ║ ║ ╚╦═╝ - 1095.296 - 0x7fc115ac3550(0) ║ └╦╝ ║ ║ ║ ║ ║ - 1308.836 - 0x7fc115ac3da0(0) ║ ╚═╦╝ ║ ║ ║ ║ - 1537.139 - 0x7fc115ac3cc0(0) ║ ║ ╚╦╝ ║ ║ - 2343.626 - 0x7fc115ac3710(0) ║ ╚═╦═╝ ║ ║ - 4022.131 - 0x7fc115ac3c50(0) ╚╦═════╝ ║ ║ - 9556.383 - 0x7fc115ac3860(0) ┬ ║ ║ ║ - 11723.55 - 0x7fc115ac3a20(0) │ ╚═════════╦╝ ║ - 17112.11 - 0x7fc115ac3b00(0) │ ╚═╦═╝ - 17796.83 - 0x7fc115ac3be0(0) └┬─────────────┘ - 25882.26 - 0x7fc115ac3470(0) ╦ ╦ ╦ ╦ ╦ ╦ ╦ ╦ ╦ ╦ - 0 - 1:0x7fc115ac3010(0) 7:0x7fc115ac34e0(0) 6:0x7fc115ac3400(0) 8:0x7fc115ac35c0(0) 9:0x7fc115ac36a0(0) 2:0x7fc115ac3080(0) 4:0x7fc115ac3240(0) 5:0x7fc115ac3320(0) 3:0x7fc115ac3160(0) 10:0x7fc115ac3780(0) ║ ║ ║ ║ ║ ║ ║ ║ ╚╦╝ - 563.7877 - 0x7fc115ac38d0(0) ║ ║ ║ ║ ║ ║ ║ ╚╦═╝ - 647.5188 - 0x7fc115ac3e80(0) ║ ┬ ║ ║ ║ ║ ║ ║ ║ - 716.3593 - 0x7fc115ac3390(0) old ║ │ ║ ║ ║ ║ ║ ╚╦═╝ - 1095.296 - 0x7fc115ac3550(0) ║ └╦╝ ║ ║ ║ ║ ║ - 1308.836 - 0x7fc115ac3da0(0) ║ ╚═╦╝ ║ ║ ║ ║ - 1537.139 - 0x7fc115ac3cc0(0) ║ ║ ╚╦╝ ║ ║ - 2343.626 - 0x7fc115ac3710(0) ║ ╚═╦═╝ ║ ║ - 4022.131 - 0x7fc115ac3c50(0) ╚╦═════╝ ║ ║ - 9556.383 - 0x7fc115ac3860(0) ┬ ║ ║ ║ - 11723.55 - 0x7fc115ac3a20(0) │ ╚═════════╦╝ ║ - 17112.11 - 0x7fc115ac3b00(0) │ ╚═╦═╝ - 17796.83 - 0x7fc115ac3be0(0) └┬─────────────┘ - 25882.26 - 0x7fc115ac3470(0) — Reply to this email directly or view it on GitHub https://github.com/luntergroup/smcsmc/issues/31#issuecomment-150259865.

shajoezhu commented 8 years ago

Fixed by PR #32